[PRE REVIEW]: BisPy: Bisimulation in Python

[whedon]

Submitting author: @fAndreuzzi (Francesco Andreuzzi) Repository: https://github.com/fAndreuzzi/BisPy Version: 0.2.0 Editor: @mjsottile Reviewers: @zoometh, @mschordan, @jonjoncardoso Managing EiC: Kristen Thyng

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Author instructions

Thanks for submitting your paper to JOSS @fAndreuzzi. Currently, there isn't an JOSS editor assigned to your paper.

@fAndreuzzi if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

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[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

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@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (629.8 files/s, 80906.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          34           1168           1218           3694
Markdown                         2             77              0            254
reStructuredText                13            112            148            192
TeX                              1              7              0             74
YAML                             2              6              6             48
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            55           1382           1380           4303
-------------------------------------------------------------------------------

Statistical information for the repository '3063ec0fbb6af9ebc92943e3' was
gathered on 2021/07/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Francesco Andreuzzi              4           204            100            0.60
francescoandreuzzi             399         28541          22022           99.40

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Francesco Andreuzzi        6104         2992.2          3.7               10.98

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1007/3-540-44585-4_8 may be a valid DOI for title: A fast bisimulation algorithm
- 10.1109/swat.1971.10 may be a valid DOI for title: Depth-first search and linear graph algorithms
- 10.1016/b978-0-12-417750-5.50022-1 may be a valid DOI for title: An n log n algorithm for minimizing states in a finite automaton
- 10.1137/0216062 may be a valid DOI for title: Three partition refinement algorithms
- 10.1007/978-3-540-77050-3_17 may be a valid DOI for title: An incremental bisimulation algorithm
- 10.1016/0898-1221(81)90008-0 may be a valid DOI for title: A strong-connectivity algorithm and its applications in data flow analysis
- 10.1145/800221.806724 may be a valid DOI for title: CCS expressions, finite state processes, and three problems of equivalence

INVALID DOIs

- None

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[fandreuz]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
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@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

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@whedon check references

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[fandreuz]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/3-540-44585-4_8 is OK
- 10.1023/A:1027328830731 is OK
- 10.1137/0201010 is OK
- 10.1137/0216062 is OK
- 10.1007/978-3-540-77050-3_17 is OK
- 10.1016/0898-1221(81)90008-0 is OK
- 10.1016/0890-5401(90)90025-D is OK

MISSING DOIs

- None

INVALID DOIs

- 10.5555/891883 is INVALID

[fandreuz]

@whedon check references

[whedon]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1007/3-540-44585-4_8 is OK
- 10.1023/A:1027328830731 is OK
- 10.1137/0201010 is OK
- 10.1016/B978-0-12-417750-5.50022-1 is OK
- 10.1137/0216062 is OK
- 10.1007/978-3-540-77050-3_17 is OK
- 10.1016/0898-1221(81)90008-0 is OK
- 10.1016/0890-5401(90)90025-D is OK

MISSING DOIs

- None

INVALID DOIs

- None

[fandreuz]

I suggest jonjoncardoso, zoometh, jkbren, TomKellyGenetics, vinodkahuja, sudarshansudarshan (graph theory).

[kthyng]

Hi @mjsottile would you be a good fit for this submission?

[kthyng]

@whedon invite @mjsottile as editor

[whedon]

@mjsottile has been invited to edit this submission.

[fandreuz]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[mjsottile]

@kthyng Sorry for the delay - my mail filter shuffled the invite into a folder I don't read daily. I'd be happy to handle this submission.

[mjsottile]

@whedon assign me as editor

[whedon]

OK, the editor is @mjsottile

[fandreuz]

Hi @mjsottile, thank you for accepting to review my submission.

[mjsottile]

Hi @fAndreuzzi : I have found one reviewer via email and will reach out to others on here to find one or two more. In the meantime, I looked at the paper and it has a few typos (e.g., line 41 - I assume "parse" should be "sparse"?). I would recommend doing a proofreading pass to find simple errors like that. It might also be worth adding a small example in the paper that demonstrates the package so a reader can get a sense for it without having to go look at code right away.

I expect I will be able to start the formal review soon once I have the additional reviewer(s).

[mjsottile]

:wave: Hello @jkbren, @zoometh, @jonjoncardoso : you were suggested by the author of this submission to the Journal of Open Source Software (JOSS) as potential reviewers. Would you be interested in providing a review? If you haven't reviewed for JOSS before, you can see the review criteria here : https://joss.readthedocs.io/en/latest/review_criteria.html

Please let me know if you are interested or have any questions.

[fandreuz]

I would recommend doing a proofreading pass to find simple errors like that.

• [x] Thank you @mjsottile, I will review the paper again to fix instanced of this kind of typo.

It might also be worth adding a small example

• [x] Sure, I'm going to add a meaningful example.

[fandreuz]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[zoometh]

@mjsottile thank you for the proposal, I'll do the review

[fandreuz]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[jonjoncardoso]

Yes, you can count me in for the review

[fandreuz]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[mjsottile]

Hi @fAndreuzzi : let me know when you've finished updating the paper so I can start the review.

[fandreuz]

Hi @mjsottile, I finished updating the paper, let me know if there's something else I should do.

[mjsottile]

@whedon assign @zoometh as reviewer

[whedon]

OK, @zoometh is now a reviewer

[mjsottile]

@whedon add @mschordan as reviewer

[whedon]

OK, @mschordan is now a reviewer

[mjsottile]

@whedon add @jonjoncardoso as reviewer

[whedon]

OK, @jonjoncardoso is now a reviewer

[mjsottile]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3519.